Wednesday, August 14, 2013

Denisova DNA

The genome sequence of a Denisovan individual was generated from a small fragment of a finger bone discovered in Denisova Cave in southern Siberia in 2008. Approximately 30-fold coverage of the genome was generated using the Illumina GAIIx sequencing platform.

This project aims to convert the massive amount of data of Denisovan Genome to a raw data download file if FTDNA (or) 23andMe did the test. So, basically, I am just extracting the SNPs from Denisovan Genome and constructing the autosomal raw data file. This project is aimed to be more like factoids provided by FTDNA, just doing it from a hobbyist research perspective (and may produce scientific results). So, if you have a long strand/segment match which suggests that you are a cousin to Denisovan, don't blame me ;). The source files are taken from Denisovan DNA in VCF format. I used 2 laptops running 24/7 for nearly 2 weeks to parse ~ 1 terrabyte of Denisovan genome to produce the below results.

  • GEDMatch# F999903 (FTDNA SNPs)
  • Download from Google Drive.
The download pages in Max-Planck-Gesellschaft mentions: When using this genome data please cite the following publication:
Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prufer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andres AM, Eichler EE, Slatkin M, Reich D, Kelso J, Paabo S: A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science. Aug 31 2012.

References / Data Used